With the massive nerfs to MR, I could see this being too powerful since its now decent mid game as well

At 200 AP, the old Lichbane would do more, but Armor vs MR is a big difference as well
A average champ will have 80 armor and 40 MR and a Tank will have around 200 armor and 100 MR

so I think this Lichbane will be better overall because its magic damage now

Actually, the mixed damage potential of Lich Bane was a part of what made it so strong before. Having an additional 1.0 AP-scaling physical damage nuke whenever you spellcast was extremely powerful, particularly if enemies were stacking MR against you. Between that and the MR removal, Lich Bane definitely lost some utility in the transition to Season 3.

But now its damage scales extremely well with your magic penetration, and enemies tend to have a lot less mr than armor especially with the recent resistance nerfs. 50 base +75% scaling is still very strong, and the new mastery spellsword improves its scaling to 80% +50.

As long as you aren't the only person on your team doing well, (so the whole enemy team is building mr against you) the new lich bane should be able to do considerably more damage on average.

How often does MR stacking occur though, really?

Jungle itemizes for armor---bot lane and supports itemize for armor, and top lane itemizes for armor unless its' an AP top---that leaves pretty much the AP mid the only one who is going to itemize for MR against you.

Will it happen, eventually? Yes, but the stacking will be nowhere near the level of armor stacking.

With a few exceptions, you'll be lucky to see over 130 MR in a match---over 200 armor, on the other paw is not, at all, uncommon.